Massilia shenzhen sp. nov., isolated from blood of one premature infant, causing sepsis

This study explores a premature infant with respiratory failure and pneumonia, suggestive of neonatal sepsis. Despite initially negative clinical specimens, blood testing revealed a pathogen. MALDI-TOF-MS and physiological tests initially failed to identify it accurately. Subsequent analysis of the 16S rRNA gene, housekeeping genes, and whole genome sequencing placed it in the genus Massilia. Average Nucleotide Identities (ANIs) indicated 88.47 % similarity with the type strain of Massilia norwichensis. Detailed characterization showed it as Gram-negative, aerobic, flagellated, measuring 0.45-0.55 × 1.75-2.40 μm. Major fatty acids included C16:0, C16:1ω7c, C18:1ω7c, and cyclo-C17:0. Minimum inhibitory concentrations to ceftazidime, penicillin, and meropenem were <0.032 μg/mL, ≤0.75 μg/mL, and <0.002 μg/mL respectively. Phylogenetic analysis, fatty acid composition, and physiological parameters confirmed it as Massilia shenzhen sp. nov., with strain GZ0329T. Given limited research on Massilia drug resistance, ceftazidime and imipenem show promise in treating Massilia infections.

Description of Massilia orientalis sp. nov., Isolated from Rhizosphere Soil of Ageratina adenophora

A novel bacteria strain, designated YIM B02787T, was isolated from rhizosphere soil of Ageratina adenophora, in Yunnan, southwest China. The strain was aerobic, Gram-stain-negative, rod-shaped and motile with one polar flagellum. Growth occurred at 4-45 °C (optimum, 20-30 °C) and pH 6.0-10.0 (optimum, 7.0-8.0), and in presence of 0-1% (w/v) NaCl. Phylogenetic analyses based on both 16S rRNA gene and genome sequences data revealed that strain YIM B02787T belongs to the genus Massilia, being closely related to Massilia phosphatilytica KCTC 52513T (98.93% similarity), M. putida KCTC 42761T (98.86%), and M. kyonggiensis JCM 19189T (98.78%). The DNA G+C content was 65.9%. The digital DNA-DNA hybridization and average nucleotide identity values between the isolate strain and aforementioned closely neighbors were low, at 35.8-48.9 and 88.5-92.5%, respectively. Strain YIM B02787T contained Q-8 as the ubiquinone and major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 45.5%) and C16:0 (27.5%). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids, and one unidentified polar lipid. On the basis of its phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM B02787Trepresents a novel species of the genus Massilia, for which the name Massilia orientalis sp. nov. is proposed. The type strain is YIM B02787T (= NBRC 116628T = CGMCC 1.61539T).

Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil

A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA-DNA hybridization between them were found to be 58.5 % (54.9-62.0 %), 53.2 % (49.8-56.7 %), 31.9 % (28.6-35.5 %), and 57.7 % (54.1-61.2 %), respectively, which were lower than the accepted threshold values of 95-96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).

Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash

The baijiu fermentation environment hosts a variety of micro-organisms, some of which still remain uncultured and uncharacterized. In this study, the isolation, cultivation and characterization of three novel aerobic bacterial strains are described. The cells of strain REN20T were Gram-negative, strictly aerobic, motile and grew at 26-37 °C, at pH 6.0-9.0 and in the presence of 0-5.0   % (w/v) NaCl. The cells of strain REN29T were Gram-negative, strictly aerobic, motile and grew at 15-30 °C, at pH 6.0-9.0 and in the presence of 0-10.0   % (w/v) NaCl. The cells of strain REN33T were Gram-positive, strictly aerobic, motile and grew at 15-37 °C, at pH 5.0-10.0 and in the presence of 0-7.0   % (w/v) NaCl. The digital DNA-DNA hybridization and average nucleotide identity by orthology values between type strains in related genera and REN20T (20.3-36.8 % and 79.8-89.9  %), REN29T (20.3-36.8  % and 74.5-88.5  %) and REN33T (22.6-48.6  % and 75.8-84.2  %) were below the standard cut-off criteria for the delineation of bacterial species, respectively. Based on polyphasic taxonomy analysis, we propose three new species, Bosea beijingensis sp. nov. (=REN20T=GDMCC 1.2894T=JCM 35118T), Telluria beijingensis sp. nov. (=REN29T=GDMCC 1.2896T=JCM 35119T) and Agrococcus beijingensis sp. nov. (=REN33T=GDMCC 1.2898T=JCM 35164T), which were recovered during cultivation and isolation from baijiu mash.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov

Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

Examining the microbial composition of natural springs in Bhaderwah, Jammu and Kashmir, India

Natural springs are the main source of water supply for domestic and agricultural use for humans living in the mountainous regions of Asia. Increasing anthropogenic activities with associated waste load, coupled with inadequate sanitation, and contamination of natural water resources and the environment are emerging as important public health issues. We performed a prospective microbiological and physicochemical investigation of water samples from seven distinct natural springs situated at an altitude of 1615 m in the Bhaderwah region of Jammu and Kashmir, India. Bacterial groups belonging to opportunistic pathogens such as members of Moraxellaceae (Acinetobacter), Arcobacteraceae (Pseudoarcobacter), Pseudomonadaceae (Pseudomonas), Oxalobacteraceae (Massilia), and Flavobacteriaceae (Flavobacterium) were observed. The total coliform test indicated an intermediate level of risk of fecal contamination of the springs, except for one site. Through a questionnaire-based survey of the local population, we discovered that around 40% of participants had suffered from waterborne diseases including typhoid (~14%) and diarrhea (~11%). Our data suggests that increased surveillance of fecal contamination and heterotrophic opportunistic pathogens is needed to enhance water quality and reduce health risks for people living in mountainous regions.

Diversity analysis of the endosymbiotic bacterial community in field-collected Haemaphysalis ticks on the tropical Hainan Island, China

Ticks are important vectors of various pathogens that cause infectious diseases in humans. Endosymbiotic bacteria have been explored as targets for tick and tick-borne disease control. However, the tick bacterial community on Hainan Island, which is the largest tropical island in China and has an environment favourable to ticks, has not yet been studied. In this study, we surveyed the bacterial community of ticks collected from grass in one village in Haikou. A total of 20 ticks were morphologically and molecularly identified as Haemaphysalis spp. The tick bacterial 16S rRNA hypervariable region amplicon libraries were sequenced on an Illumina MiSeq platform. A total of 10 possible bacterial genera were detected, indicating a low-diversity bacterial community profile. The dominant bacterial genus, Massilia, accounted for 97.85% of the population. Some other bacterial genera, including Arsenophonus and Pseudomonas, have been reported to play a role in tick development and tick-borne pathogen transmission in other tick species. Overall, the study highlights the first descriptive understanding of the tick bacterial community on Hainan Island and provides a basis for deciphering the interactions between the tick microbiome and tick-borne pathogens.

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers

Two aerobic, Gram-stain-negative, motile, mesophilic, rod-shaped and catalase-positive bacterial strains designated AF9R3T and GN2-R2T were isolated from flowers collected in the Republic of Korea. Strain AF9R3T grew at 4–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v), and strain GN2-R2T grew at 10–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strains AF9R3T and GN2-R2T belonged to the genera Duganella and Massilia , respectively, showing high sequence similarity to Duganella levis CY42WT (99.4 %) and Massilia putida 6 NM-7T (98.0 %), respectively. Both strains contained summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 as the major fatty acids, and ubiquinone Q-8 as the predominant quinone. Strain AF9R3T had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and strain GN2-R2T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Orthologous average nucleotide identity and digital DNA–DNA hybridization values of strain AF9R3T to its closest relative D. levis CY42WT were 92.6 and 56.5 %, and those of strain GN2-R2T to its closest relative M. putida 6 NM-7T were 81.4 and 24.8 %. Based on genotypic and phenotypic data, strains AF9R3T and GN2-R2T are considered to represent novel species of the genus Duganella and Massilia , respectively, for which the names Duganella dendranthematis sp. nov. (type strain AF9R3T=KACC 21258T=NBRC 114510T) and Massilia forsythiae sp. nov. (type strain GN2-R2T=KACC 21261T=NBRC 114511T) have been proposed.

Bacterial and fungal isolation from face masks under the COVID-19 pandemic

The COVID-19 pandemic has led people to wear face masks daily in public. Although the effectiveness of face masks against viral transmission has been extensively studied, there have been few reports on potential hygiene issues due to bacteria and fungi attached to the face masks. We aimed to (1) quantify and identify the bacteria and fungi attaching to the masks, and (2) investigate whether the mask-attached microbes could be associated with the types and usage of the masks and individual lifestyles. We surveyed 109 volunteers on their mask usage and lifestyles, and cultured bacteria and fungi from either the face-side or outer-side of their masks. The bacterial colony numbers were greater on the face-side than the outer-side; the fungal colony numbers were fewer on the face-side than the outer-side. A longer mask usage significantly increased the fungal colony numbers but not the bacterial colony numbers. Although most identified microbes were non-pathogenic in humans; Staphylococcus epidermidis, Staphylococcus aureus, and Cladosporium, we found several pathogenic microbes; Bacillus cereus, Staphylococcus saprophyticus, Aspergillus, and Microsporum. We also found no associations of mask-attached microbes with the transportation methods or gargling. We propose that immunocompromised people should avoid repeated use of masks to prevent microbial infection.

Ocular Microbiome in a Group of Clinically Healthy Horses

The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional techniques, which has limited the depth of the knowledge on the subject. The objective of this study was to characterize and predict the metabolic pathways of the ocular microbiome of a group of healthy horses. Conjunctival swabs were obtained from both eyes of 14 horses, and DNA extraction was performed from the swabs, followed by next generation sequencing and bioinformatics analyses employing DADA2 and PICRUSt2. A total of 17 phyla were identified, of which Pseudomonadota (Proteobacteria) was the most abundant (59.88%), followed by Actinomycetota (Actinobacteria) (22.44%) and Bacteroidota (Bacteroidetes) (16.39%), totaling an average of 98.72% of the communities. Similarly, of the 278 genera identified, Massilia, Pedobacter, Pseudomonas, Sphingomonas, Suttonella and Verticia were present in more than 5% of the samples analyzed. Both Actinobacteria and Bacteroides showed great heterogeneity within the samples. The most abundant inferred metabolic functions were related to vital functions for bacteria such as aerobic respiration, amino acid, and lipid biosynthesis.

Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov

A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).

Blood microbiome is associated with changes in portal hypertension after successful direct-acting antiviral therapy in patients with HCV-related cirrhosis

BACKGROUND

Patients with a significant decrease in hepatic venous pressure gradient (HVPG) have a considerable reduction of liver complications and higher survival after HCV eradication.

OBJECTIVES

To evaluate the association between the baseline blood microbiome and the changes in HVPG after successful direct-acting antiviral (DAA) therapy in patients with HCV-related cirrhosis.

METHODS

We performed a prospective study in 32 cirrhotic patients (21 HIV positive) with clinically significant portal hypertension (HVPG ≥10 mmHg). Patients were assessed at baseline and 48 weeks after HCV treatment completion. The clinical endpoint was a decrease in HVPG of ≥20% or HVPG <12 mmHg at the end of follow-up. Bacterial 16S ribosomal DNA was sequenced using MiSeq Illumina technology, inflammatory plasma biomarkers were investigated using ProcartaPlex immunoassays and the metabolome was investigated using GC-MS.

RESULTS

During the follow-up, 47% of patients reached the clinical endpoint. At baseline, those patients had a higher relative abundance of Corynebacteriales and Diplorickettsiales order, Diplorickettsiaceae family, Corynebacterium and Aquicella genus and Undibacterium parvum species organisms and a lower relative abundance of Oceanospirillales and Rhodospirillales order, Halomonadaceae family and Massilia genus organisms compared with those who did not achieve the clinical endpoint according to the LEfSe algorithm. Corynebacteriales and Massilia were consistently found within the 10 bacterial taxa with the highest differential abundance between groups. Additionally, the relative abundance of the Corynebacteriales order was inversely correlated with IFN-γ, IL-17A and TNF-α levels and the Massilia genus with glycerol and lauric acid.

CONCLUSIONS

Baseline-specific bacterial taxa are related to an HVPG decrease in patients with HCV-related cirrhosis after successful DAA therapy.

Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3^T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia. The closest phylogenetic relative was Massilia arenae CICC 24458^T (99.5 %), followed by M. timonae CCUG45783^T (97.9 %), M. oculi CCUG43427A^T (97.8 %), and M. aurea DSM 18055^T (97.8 %). The major fatty acids were C_16 : 0 and C_16 : 1  ω7c and/or C_16 : 1  ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3^T and Massilia arenae CICC 24458^T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3^T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3^T (=CGMCC 1.17158^T=KCTC 82193^T).

Isolation, Identification, and Characterization of Polystyrene-Degrading Bacteria From the Gut of Galleria Mellonella (Lepidoptera: Pyralidae) Larvae

Polystyrene (PS) is a widely used petroleum-based plastic, that pollutes the environment because it is difficult to degrade. In this study, a PS degrading bacterium identified as Massilia sp. FS1903 was successfully isolated from the gut of Galleria mellonella (Lepidoptera: Pyralidae) larvae that were fed with PS foam. Scanning electron microscopy and X-ray energy dispersive spectrometry showed that the structure and morphology of the PS film was destroyed by FS 1903, and that more oxygen appeared on the degraded PS film. A water contact angle assay verified the chemical change of the PS film from initially hydrophobic to hydrophilic after degradation. X-ray photoelectron spectroscopy further demonstrated that more oxygen-containing functional groups were generated during PS degradation. After 30 days of bacterial stain incubation with 0.15 g PS, 80 ml MSM, 30°C and PS of Mn 64400 and Mw 144400 Da, the weight of the PS film significantly decreased, with 12.97 ± 1.05% weight loss. This amount of degradation exceeds or is comparable to that previously reported for other species of bacteria reported to degrade PS. These results show that Massilia sp. FS1903 can potentially be used to degrade PS waste.

Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis

A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11^T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang Province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11^T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1^T (98.46%) and Massilia putida 6NM-7 ^T (98.41%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11^T formed lineage related to M. phosphatilytica 12-OD1^T and M. putida 6NM-7 ^T. The major fatty acids of the strain were C_16:0, C_17:0-cyclo and C_16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11^T and M. phosphatilytica 12-OD1^T and M. putida 6NM-7 ^T were 45.4 and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11^T was 66.2%. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to have the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, we conclude that strain NEAU-DD11^T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11^T (= CCTCC AB 2019141 ^T = DSM 109721 ^T).

Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19^T was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19^T formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. violaceinigra B2^T (98.6% sequence similarity), M. eurypsychrophilia JCM 30074^T (98.3%) and M. atriviolacea SOD^T (98.1%). The only respiratory quinone was ubiquinone-8. The principal cellular fatty acids were summed feature 3 (iso-C_15:0 2-OH/C_16:1ω7c) and C_16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain was 63.2%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RP-1-19^T and closest members were ≤ 80 and 23.2%, respectively. The genome was 4,522,469 bp long with 30 scaffolds and 4076 protein-coding genes. The genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome analysis revealed the presence of cold-shock proteins CspA and CspC. Presence of cspA and cspC genes in the genome manifest ecophysiology of strain RP-1-19^T that may help in cold-adaptation. Based on these data, strain RP-1-19^T represents a novel species in the genus Massilia, for which the name Massilia polaris sp. nov. is proposed. The type strain is RP-1-19^T (= KACC 21619^T = NBRC 114359^T).

Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1^T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1^T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33^T (98.8% sequence similarity), M. putida 6NM-7^T (98.6%), M. arvi THG-RS2O^T (98.5%), M. phosphatilytica 12-OD1^T (98.3%) and M. niastensis 5516S-1^T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1^T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1^T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1^T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1^T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1^T (= KACC 21627^T = NBRC 114363^T).

No evidence for a placental microbiome in human pregnancies at term

BACKGROUND

The placenta plays an important role in the modulation of pregnancy immunity; however, there is no consensus regarding the existence of a placental microbiome in healthy full-term pregnancies.

OBJECTIVE

This study aimed to investigate the existence and origin of a placental microbiome.

STUDY DESIGN

A cross-sectional study comparing samples (3 layers of placental tissue, amniotic fluid, vernix caseosa, and saliva, vaginal, and rectal samples) from 2 groups of full-term births: 50 women not in labor with elective cesarean deliveries and 26 with vaginal deliveries. The comparisons were performed using polymerase chain reaction amplification and DNA sequencing techniques and bacterial culture experiments.

RESULTS

There were no significant differences regarding background characteristics between women who delivered by elective cesarean and those who delivered vaginally. Quantitative measurements of bacterial content in all 3 placental layers (quantitative polymerase chain reaction of the 16S ribosomal RNA gene) did not show any significant difference among any of the sample types and the negative controls. Here, 16S ribosomal RNA gene sequencing of the maternal side of the placenta could not differentiate between bacteria in the placental tissue and contamination of the laboratory reagents with bacterial DNA. Probe-specific quantitative polymerase chain reaction for bacterial taxa suspected to be present in the placenta could not detect any statistically significant difference between the 2 groups. In bacterial cultures, substantially more bacteria were observed in the placenta layers from vaginal deliveries than those from cesarean deliveries. In addition, 16S ribosomal RNA gene sequencing of bacterial colonies revealed that most of the bacteria that grew on the plates were genera typically found in human skin; moreover, it revealed that placentas delivered vaginally contained a high prevalence of common vaginal bacteria. Bacterial growth inhibition experiments indicated that placental tissue may facilitate the inhibition of bacterial growth.

CONCLUSION

We found no evidence to support the existence of a placental microbiome in our study of 76 term pregnancies, which used polymerase chain reaction amplification and sequencing techniques and bacterial culture experiments. Incidental findings of bacterial species could be due to contamination or to low-grade bacterial presence in some locations; such bacteria do not represent a placental microbiome per se.

Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure

BACKGROUND

In industrialized countries, non-communicable diseases have been increasing in prevalence since the middle of the 20th century. While the causal mechanisms remain poorly understood, increased population density, pollution, sedentary behavior, smoking, changes in diet, and limited outdoor exposure have all been proposed as significant contributors. Several hypotheses (e.g. Hygiene, Old Friends, and Biodiversity Hypotheses) also suggest that limited environmental microbial exposures may underpin part of this rise in non-communicable diseases. In response, the Microbiome Rewilding Hypothesis proposes that adequate environmental microbial exposures could be achieved by restoring urban green spaces and could potentially decrease the prevalence of non-communicable diseases. However, the microbial interactions between humans and their surrounding environment and the passaging of microbes between both entities remains poorly understood, especially within an urban context.

RESULTS

Here, we survey human skin (n = 90 swabs) and nasal (n = 90 swabs) microbiota of three subjects that were exposed to air (n = 15), soil (n = 15), and leaves (n = 15) from different urban green space environments in three different cities across different continents (Adelaide, Australia; Bournemouth, United Kingdom; New Delhi, India). Using 16S ribosomal RNA metabarcoding, we examined baseline controls (pre-exposure) of both skin (n = 16) and nasal (n = 16) swabs and tracked microbiota transfer from the environment to the human body after exposure events. Microbial richness and phylogenetic diversity increased after urban green space exposure in skin and nasal samples collected in two of the three locations. The microbial composition of skin samples also became more similar to soil microbiota after exposure, while nasal samples became more similar to air samples. Nasal samples were more variable between sites and individuals than skin samples.

CONCLUSIONS

We show that exposure to urban green spaces can increase skin and nasal microbial diversity and alter human microbiota composition. Our study improves our understanding of human-environmental microbial interactions and suggests that increased exposure to diverse outdoor environments may increase the microbial diversity, which could lead to positive health outcomes for non-communicable diseases.

Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths

Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2^T and Massilia atriviolacea SOD^T and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094^T=CCM 8692^T=LMG 31213^T), Massilia aquatica sp. nov. (P3165^T=CCM 8693^T=LMG 31211^T), Massilia mucilaginosa sp. nov. (P5902^T=CCM 8733^T=LMG 31210^T), and Massilia frigida sp. nov. (P5534^T=CCM 8695^T=LMG 31212^T).

Massilia arenae sp. nov., isolated from sand soil in the Qinghai–Tibetan Plateau

A bacterial strain, designated GEM5T, was isolated from sand soil samples from the Qinghai–Tibet Plateau. The polyphasic study confirmed the affiliation of the isolate with the genus Massilia . GEM5T had Gram-stain-negative, non-spore-forming and rod-shaped cells and grew at 4–30 °C, pH 6–8 and with 0–2 % (w/v) NaCl. Its cell wall contained ribose. Q8 was the predominant respiratory quinone, and summed feature 3 (C16 : 1ω6c/ω7c) and C16 : 0 were the major components of the fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The DNA G+C content was 65.1 mol%. The phylogenetic analysis based on the 16S rRNA gene showed a stable clade being formed by GEM5T, Massilia timonae CCUG 45783T (97.94 %) and Massilia oculi CCUG 43427AT (97.58 %). The average nucleotide identity (ANIb) values between GEM5T and M. timonae CCUG 45783T, M.oculi CCUG 43427AT were 91.3 and 91.7 %, respectively. On the basis of the morphological, physiological and chemotaxonomic pattern, it was proposed that strain GEM5T (=JCM 32744T=CICC 24458T) should be classified as representing a member of the genus Massilia with the name Massilia arenae sp. nov.

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing

Black patinas are very common biological deterioration phenomena on lapideous artworks in outdoor environments. These substrates, exposed to sunlight, and atmospheric and environmental agents (i.e. wind and temperature changes), represent extreme environments that can only be colonized by highly versatile and adaptable microorganisms. Black patinas comprise a wide variety of microorganisms, but the morphological plasticity of most of these microorganisms hinders their identification by optical microscopy. This study used Next-Generation Sequencing (NGS) (including shotgun and amplicon sequencing) to characterize the black patina of the travertine embankments (muraglioni) of the Tiber River in Rome (Italy). Overall, the sequencing highlighted the rich diversity of bacterial and fungal communities and allowed the identification of more than one hundred taxa. NGS confirmed the relevance of coccoid and filamentous cyanobacteria observed by optical microscopy and revealed an informative landscape of the fungal community underlining the presence of microcolonial fungi and phylloplane yeasts. For the first time high-throughput sequencing allowed the exploration of the expansive diversity of bacteria in black patina, which has so far been overlooked in routine analyses. Furthermore, the identification of euendolithic microorganisms and weathering agents underlines the biodegradative role of black patina, which has often been underestimated. Therefore, the use of NGS to characterize black patinas could be useful in choosing appropriate conservation treatments and in the monitoring of stone colonization after the restoration interventions.

Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427T (=DSM 26321T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains

Massilia oculi sp. nov. of type strain CCUG 43427^T is a Gram-negative, rod-shaped, nonspore-forming bacterium, which was recently isolated from the eye of a patient suffering from endophthalmitis and was described as novel species in Massilia genus. In this study, we present the complete genome sequence of this strain by using Pacbio SMRT cell platform and compare this sequence with the genomes of 30 Massilia representative strains. Also, a comprehensive search was conducted for genes and proteins involved in antibiotic resistance and pathogenicity. The genome of CCUG 43427^T is 5,844,653 bp with 65.55% GC content. This genome contains four prophages and four genomic islands (GIs). The cobalt/zinc/cadmium transporter locus CzcABCD is included in these GIs. This GI was predicted to play important role in bacterial heavy-metal tolerance. The in silico genome analysis also revealed that this strain contains a lot of antibiotic resistance and pathogenicity related genes. This result suggested that this strain may has evolved a wide arsenal of weapons for pathogenicity and survival. Genome comparison among CCUG 43427^T and other 30 Massilia strains revealed that more than 400 genes are unique in CCUG 43427^T. Among these, one gene cluster, which was annotated to be important for LOS biosynthesis, catalytic mechanism and the substrate specificity of the enzyme, was predicted to be horizontally transferred by using phylogenies and biased GC content.

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Massilia glaciei sp. nov., isolated from the Muztagh Glacier

A Gram-stain-negative, rod-shaped, bacterial strain, B448-2^T, was isolated from an ice core from the Muztagh Glacier, on the Tibetan Plateau. B448-2^T grew optimally at pH 7.0 and 20 °C in the presence of 0-1.0 % (w/v) NaCl. The results of 16S rRNA gene sequence similarity analysis indicated that B448-2^T was closely related to Massilia eurypsychrophila CGMCC 1.12828^T, Rugamonas rubra CCM3730^T and Duganella zoogloeoides JCM20729^T at levels of 97.8, 97.7  and 97.3 %, respectively. The predominant fatty acids of B448-2^T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of the strain was 66.1 mol%. In DNA-DNA hybridization tests, B448-2^T shared 37.6 % DNA-DNA relatedness with Massilia eurypsychrophila CGMCC 1.12828^T. On the basis of the results for phenotypic and chemotaxonomic characteristics, B448-2^T was considered to represent a novel species of the genus Massilia, for which the name Massiliaglaciei sp. nov. is proposed. The type strain is B448-2^T (=JCM 30271^T=CGMCC 1.12920^T).

Massilia agri sp. nov., isolated from reclaimed grassland soil

A light yellow-coloured, Gram-stain-negative, motile and rod-shaped bacterium, designated strain K-3-1T, was isolated from reclaimed grassland soils of Belbari, Morang, Nepal. It was able to grow at 4-45 °C, at pH 5.0-10.0, and at 0-2 % (w/v) NaCl concentrations. This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain K-3-1T belongs to the genus Massilia and is closely related to Massilia consociata CCUG 58010T (98.3 % sequence similarity), Massilia tieshanensis TS3T (98.1 % sequence similarity), Massilia kyonggiensis TSA1T (98.1 % sequence similarity), Massilia yuzhufengensisY1243-1T (98.1 % sequence similarity), Massilia haematophila CCUG 38318T (98.0 % sequence similarity), Massilia varians CCUG 35299T (97.9 % sequence similarity), Massilia niastensis 5516 S-1T (97.6 % sequence similarity) and Massilia alkalitolerans YIM 31775T (97.5 % sequence similarity). The predominant respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain K-3-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0, C10 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The genomic DNA G+C content of this novel strain was 66.8 mol%. The DNA-DNA relatedness between strain K-3-1T and its closest reference strains were significantly lower than the threshold value of 70 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-1T represents a novel species of the genus Massilia, for which the name Massilia agri sp. nov. is proposed. The type strain is K-3-1T (=KEMB 9005-446T=KACC 19000T=JCM 31661T).

Massilia varians Isolated from a Clinical Specimen

We report a case of Massilia varians isolated from a deep finger wound following orthopedic surgery on an immunocompetent patient. The bacterium was identified by 16S rDNA sequence analysis. This is the first case of M. varians isolated from a clinical specimen since the first report in 2008.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Massilia psychrophila sp. nov., isolated from an ice core

A Gram-stain-negative, aerobic, rod-shaped, motile bacterium, strain B1555-1T, was isolated from an ice core drilled from Ulugh Muztagh Glacier, China. The optimum growth temperature of strain B1555-1T was 15 °C and optimum pH was 7. The major fatty acids of strain B1555-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain B1555-1T was 66.0 mol%. In 16S rRNA gene sequence comparisons, strain B1555-1T was affiliated to the genus Massilia and shared 98.30 and 97.13 % similarity with Massilia eurypsychrophila B528-3T and Massilia niabensis 5420S-26T, respectively. The results of DNA-DNA hybridization revealed that strain B1555-1T showed 49.8 % relatedness with M. eurypsychrophila B528-3T and 38.5 % with M. niabensis 5420S-26T. Based on the genotypic and phenotypic evidence presented in this study, strain B1555-1T represents a novel species of the genus Massilia, for which the name Massilia psychrophila sp. nov. is proposed. The type strain is B1555-1T (=CGMCC 1.15196T=JCM 30813T).

Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia

A novel bacterial strain, designated THG-RS2OT, was isolated from fallow-land soil previously cultivated with Brassica oleracea in Yongin, South Korea. Cells were Gram-stain-negative, aerobic, non-motile rods, catalase- and oxidase-positive. Strain THG-RS2OT grew optimally at 25–37 °C, at pH 7.0 and in the absence of NaCl. 16S rRNA gene sequence analysis demonstrated that strain THG-RS2OT shows highest sequence similarity with Massilia kyonggiensis KACC 17471T followed by Massilia aerilata KACC 12505T, Massilia niastensis KACC 12599T, Massilia tieshanensis KACC 14940T and Massilia haematophila KCTC 32001T. Levels of DNA–DNA relatedness between strain THG-RS2OT and the closest phylogenetic neighbours were below 55.0 % and the DNA G+C content of strain THG-RS2OT was 63.2 mol%. Major fatty acids were C16 : 0, cyclo-C17 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was identified as ubiquonone-8 and predominant polar lipids were determined to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Characterization by 16S rRNA gene sequence analysis, DNA–DNA hybridization, ubiquinone, polar lipid, fatty acid composition, and physiological and biochemical parameters revealed that strain THG-RS2OT represents a novel species of the genus Massilia. Hence, the present study describes a novel species for which the name Massilia arvi sp. nov. is proposed. The type strain is THG-RS2OT ( = KCTC 42609T = CCTCC AB 2015115T).

Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core

Strain B528-3T, a Gram-stain-negative, rod-shaped, aerobic, facultatively psychrophilic bacterium with polar flagella, was isolated from an ice core drilled from Muztagh Glacier, Xinjiang, China. The novel isolate was classified into the genus Massilia. The 16S rRNA gene sequence of the novel isolate shares a pairwise similarity of less than 97 % with those of all the type strains of the genus Massilia. The major fatty acids of strain B528-3T were summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) (57.31 %), C16:0 (11.46 %) and C18:1ω7c (14.72 %). The predominant isoprenoid quinone was Q-8. The DNA G+C content was 62.2 mol% (T m). The major polar lipids of this bacterium were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. From the genotypic and phenotypic data, it is evident that strain B528-3T represents a novel species of the genus Massilia, for which the name Massilia eurypsychrophila sp. nov. is proposed. The type strain is B528-3T ( = JCM 30074T = CGMCC 1.12828T).

Massilia norwichensis sp. nov., isolated from an air sample

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9(T), isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9(T) identified Massilia haematophila CCUG 38318(T), M. niastensis 5516S-1(T) (both 97.7% similarity), M. aerilata 5516S-11(T) (97.4%) and M. tieshanensis TS3(T) (97.4%) as the next closest relatives. In partial gyrB and lepA sequences, NS9(T) shared the highest similarities with M. haematophila CCUG 38318(T) (94.5%) and M. aerilata 5516-11(T) (94.3%), respectively. These sequence data demonstrate the affiliation of NS9(T) to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9(T) to the genus Massilia. Major fatty acids were summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH), C16:0, C18: 1ω7c and C10:0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA-DNA hybridizations demonstrate that strain NS9(T) is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9(T) ( = CCUG 65457(T) =LMG 28164(T)).

Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm

A bacterial strain, designated strain LP01(T), was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain-negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472(T) and M. lutea DSM 17473(T). DNA-DNA hybridization showed low relatedness of strain LP01(T) to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia. The DNA G+C content was 66.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study suggest that strain LP01(T) represents a novel species of the genus Massilia, for which the name Massilia umbonata sp. nov. is proposed. The type strain is LP01(T) ( = CECT 7753(T) = DSM 26121(T)).

Massilia lurida sp. nov., isolated from soil

A bacterial isolate, designated strain D5T, was isolated from a soil sample collected from the Inner Mongolia Autonomous Region, China, and subjected to a taxonomic investigation using a polyphasic approach. Strain D5T was aerobic, Gram-stain-negative, rod-shaped and motile. Strain D5T fell within the evolutionary radius of the genus Massilia in the phylogenetic tree based on 16S rRNA gene sequences and was most closely related to Massilia plicata 76T with 97.3 % 16S rRNA gene sequence similarity. The predominant quinone of strain D5T was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. These chemotaxonomic data supported the affiliation of strain D5T to the genus Massilia . The genomic DNA G+C content was 65.9 mol%. Mean DNA–DNA relatedness values between strain D5T and the phylogenetically most closely related species of the genus Massilia , Massilia plicata KCTC 12344T and Massilia dura KCTC 12342T, were 26 and 21 %, respectively. Strain D5T could be differentiated from recognized species of the genus Massilia by several phenotypic characteristics. It is clear from the data presented that strain D5T represents a novel species of the genus Massilia , for which the name Massilia lurida sp. nov. is proposed. The type strain is D5T ( = CGMCC 1.10822T = KCTC 23880T).

Massilia yuzhufengensis sp. nov., isolated from an ice core

A Gram-negative, rod-shaped, aerobic, motile bacterium, strain Y1243-1T, was isolated from an ice core drilled from Yuzhufeng Glacier, Tibetan Plateau, China. Cells had polar flagella. The novel strain shared 94.7–97.6 % 16S rRNA gene sequence similarity with the type strains of species of the genus Massilia . The novel isolate is thus classified in the genus Massilia . The major fatty acids of strain Y1243-1T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (43.98 %), C16 : 0 (27.86 %), C10 : 0 3-OH (7.10 %), C18 : 0 (6.95 %) and C18 : 1ω7c (5.01 %). The predominant isoprenoid quinone was Q-8. The DNA G+C content of strain Y1243-1T was 65.7 mol% (T m). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. A number of phenotypic characteristics distinguished the novel isolate from the type strains of recognized Massilia species. Furthermore, in DNA–DNA hybridization tests, strain Y1243-1T shared 45 % relatedness with its closest phylogenetic relative, Massilia consociata CCUG 58010T. From the genotypic and phenotypic data, it is evident that strain Y1243-1T represents a novel species of the genus Massilia , for which the name Massilia yuzhufengensis sp. nov. is proposed. The type strain is Y1243-1T ( = KACC 16569T = CGMCC 1.12041T).

Massilia sp. isolated from otitis media

Common bacterial pathogens of otitis media include Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, alpha-hemolytic streptococci, and Group A streptococci. We recently isolated a gram-negative, rod-shaped, non-spore-forming bacterium from a patient with otitis media following tympanocentesis. 16S rRNA gene sequence similarity studies of effusion identified this strain (CCUG 43427AT) as Massilia sp. (99.7%). Massilia spp. have been isolated from soil, air, and immunocompromised patients. However, there are no reports of their isolation from cases of otitis media. This case report highlights a rare and novel bacterial organism of otitis media.

Massilia tieshanensis sp. nov., isolated from mining soil

A bacterial isolate, designated strain TS3T, was isolated from soil collected from a metal mine in Tieshan District, Daye City, Hubei Province, in central China. Cells of this strain were Gram-negative, motile and rod-shaped. The strain had ubiquinone Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c as the major fatty acids. The G+C content was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TS3T was most closely related to Massilia niastensis 5516S-1T (98.5 %), Massilia consociata CCUG 58010T (97.6 %), Massilia aerilata 5516S-11T (97.4 %) and Massilia varians CCUG 35299T (97.2 %). DNA–DNA hybridization revealed low relatedness between strain TS3T and M. niastensis KACC 12599T (36.5 %), M. consociata CCUG 58010T (27.1 %), M. aerilata KACC 12505T (22.7 %) and M. varians CCUG 35299T (46.5 %). On the basis of phenotypic and phylogenetic characteristics, strain TS3T belongs to the genus Massilia , but is clearly differentiated from other members of the genus. The strain represents a novel species, for which the name Massilia tieshanensis sp. nov. is proposed. The type strain is TS3T ( = CCTCC AB 2010202T  = KACC 14940T).